Ok. I'll try to cover some of the questions here. In terms of Kaiju looks, I figured it's varies. The transformation itself can be...well pretty much anything but as someone noted, there has to be crystal parts somewhere on the body of said monster to show some of the "infection". Or most parts. It's up to you. I'm keeping an open mind right now in that term. Heck, some characters may not do a full giant transformation. Perhaps they simply have special abilities without the transforming. Still, infected, depending on the individual, are built tough but enough damage or a big enough shot can kill one.
As for NPC's with your main character, I don't mind so long as you don't use too many. I don't want you to get overwhelmed with multiple points of view of different charcters. Heck, that's what I'm worried about being the host of this and I have to manage possibly multiple characters to keep the story interesting. But in terms of your "main" character cap, try to keep it to 2 at most. With NPC's...well just don't go crazy with large armies worth of them.